As a prerequisite to the Trinotate workflow, I ran an hmmscan (against the Pfam-A.hmm database) on the *.pep file generated from Transdecoder. Note that the *.pep file contains >77,000 sequences.

This is the command line I used: hmmscan --cpu 4 --domtblout TrinotatePFAM.out Pfam-A.hmm longest_orfs.pep

My question is; how and why am I getting >140,000 entries in the output file (TrinotatePFAM.out). What is confusing is that some of the query names in the output file are not even in the *.pep input file - how can that be?

Thanks!